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Following contact with the Flood, Sergeant Johnson manages to avoid being overwhelmed by infection forms. He fires at an Infection Form which has latched onto PrivateJenkins, though he fails to kill it. He watches as the Marine transforms before his eyes into a combat form. The combat form delivers a blow to Johnson's arm, throwing the sergeant out of the containment room, across a large observation chamber, and into a wall.

Several infected Marines approach Johnson, prompting him to run into a hallway. He locks the door with a spoofer and proceeds down the hallway. An infected Marine fires a shotgun at Johnson. The pellets hit the wall, missing the sergeant by inches. Johnson dives to the ground, firing the remaining rounds in his assault rifle into the combat form, ripping its head off but not killing it. He then shoots down the combat form with his pistol. He makes his way across a light bridge, jumping onto the other side just as a combat form shuts the bridge down. As he jumps across the chasm, he throws a grenade behind him. The explosion kills his pursuers, knocking him to the ground. He steps onto the lift, glad to have finally escaped the Flood.

When shot, the combat forms bleed red blood rather than the yellowish fluid seen in the games. This could be because the Marines had been recently infected, so they would not yet have undergone a full transformation.

At the beginning of the story, Johnson and his teammates appear to be in a different place inside the containment facility from the one seen in the level 343 Guilty Spark.

In the story, the Flood are able to infect the Marines in mere seconds. This behavior was not seen in-game until Halo 3.